When you use ink mark up during a show and close you have the option to discard the ink. If you decide to keep it though it's not that easy to remove in future!

Here's a tiny 12kb Add In for 2007 only which will do just that.

Make sure that macro security is set low enough to run macros. Copy the ppam file and open PowerPoint. Save As and choose type=PowerPoint Add In. In the folder that opens PASTE in the file and then just cancel the save.